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Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor:

List of all members.


Class Summary

Synopsis

Description

This version of the module is still very experimental.
 

Definition at line 21 of file GenomicAlignTreeAdaptor.pm.

Available Methods

protected _build_tree_from_nodes ()
protected _columns ()
protected _construct_sql_query ()
protected
Bio::EnsEMBL::Compara::GenomicAlign 
_create_GenomicAlign_object_from_rowhash ()
protected
Bio::EnsEMBL::Compara::GenomicAlignGroup 
_create_GenomicAlignGroup_object_from_rowhash ()
protected _default_where_clause ()
protected
Bio::EnsEMBL::Compara::GenomicAlignTree 
_fetch_by_genomic_align_block ()
protected _final_clause ()
protected Listref _generic_fetch ()
protected _get_starting_lr_index ()
protected _left_join ()
protected _list_dbIDs ()
protected _lr_table_name ()
protected Listref _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public cache_add_object ()
public cache_fetch_by_id ()
public clear_cache ()
public List columns ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
create_instance_from_rowhash ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public void default_where_clause ()
public void delete ()
public DESTROY ()
public dump_data ()
public Arrayref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Ref fetch_all_by_MethodLinkSpeciesSet ()
public Ref fetch_all_by_MethodLinkSpeciesSet_DnaFrag ()
public Ref fetch_all_by_MethodLinkSpeciesSet_Slice ()
public Reference fetch_all_children_for_node ()
public fetch_all_leaves_indexed ()
public fetch_all_roots ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
fetch_by_genomic_align_block_id ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
fetch_by_GenomicAlignBlock ()
public
Bio::EnsEMBL::Compara::NestedSet 
fetch_first_shared_ancestor_indexed ()
public Reference fetch_node_by_node_id ()
public Reference fetch_parent_for_node ()
public Reference fetch_root_by_node ()
public fetch_subroot_by_left_right_index ()
public fetch_subtree_under_node ()
public fetch_tree_at_node_id ()
public final_clause ()
public Listref generic_fetch ()
public get_dumped_data ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
init_instance_from_rowhash ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public void left_join_clause ()
public new ()
public DBI::StatementHandle prepare ()
public void set_neighbour_nodes_for_leaf ()
public Int species_id ()
public store ()
public void store_group ()
public void store_node ()
public Nothing sync_tree_leftright_index ()
public List tables ()
public update ()
public void update_neighbourhood_data ()
public update_subtree ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_build_tree_from_nodes ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_construct_sql_query ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::_create_GenomicAlign_object_from_rowhash ( )
  Args[1]    : DBI::row_hashref $hashref containing key-value pairs
  Example    : my $genomic_align = $self->_create_GenomicAlign_object_from_rowhash($rowhash);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::GenomicAlign object
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
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protected Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::_create_GenomicAlignGroup_object_from_rowhash ( )
  Args[1]    : DBI::row_hashref $hashref containing key-value pairs
  Example    :  my $genomic_align_group = $self->_create_GenomicAlignGroup_object_from_rowhash($rowhash);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::GenomicAlignGroup object
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
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protected Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::_fetch_by_genomic_align_block ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignBlock $genomic_align_block
  Example    : my $genomic_align_tree =
                  $genomic_align_tree_adaptor->fetch_by_genomic_align_block($genomic_align_block);
  Description: Internal method that is used by both fetch_all_by_GenomicAlignBlock and 
                fetch_all_by_genomic_align_block_id. Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : $object->method_name
  Status     : At risk
 
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protected Listref Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_generic_fetch ( ) [inherited]
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('WHERE contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch
 
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protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_get_starting_lr_index ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_lr_table_name ( ) [inherited]

Undocumented method

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protected Listref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::_objs_from_sth ( )
  Args[1]    : DBI::row_hashref $hashref containing key-value pairs
  Example    :   my $genomic_align_trees = $self->_objs_from_sth($sth);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::GenomicAlignTreeAdaptor object
  Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlignTree objects
  Exceptions : none
  Caller     : general
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::cache_add_object ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::cache_fetch_by_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::clear_cache ( ) [inherited]

Undocumented method

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public List Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::columns ( )
  Args       : none
  Example    : $columns = $self->columns()
  Description: a list of [tablename, alias] pairs for use with generic_fetch
  Returntype : list of [tablename, alias] pairs
  Exceptions : none
  Caller     : NestedSetAdaptor::generic_fetch
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::create_instance_from_rowhash ( )
  Args[1]    : DBI::row_hashref $hashref containing key-value pairs
  Example    : my $node = $self->create_instance_from_rowhash($rowhash);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::GenomicAlignTree object
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::default_where_clause ( )
  Args       : none
  Example    : none
  Description: a where clause for use with generic_fetch
  Returntype : none
  Exceptions : none
  Caller     : NestedSetAdaptor::generic_fetch
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::delete ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : $genomic_align_tree_adaptor->delete($root);
  Description: Method for deleting a Bio::EnsEMBL::Compara::GenomicAlignTree
               from a database. Must give the root ie does not delete
               sub-trees.
  Returntype : none
  Exceptions : none
  Caller     : none
  Status     : At risk
 
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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::DESTROY ( ) [inherited]

Undocumented method

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public Arrayref Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all ( ) [inherited]
  Arg[1]     : -none-
  Example    : $all_trees = $proteintree_adaptor->fetch_all();
  Description: Fetches from the database all the nested sets.
  Returntype : arrayref of Bio::EnsEMBL::Compara::NestedSet
  Exceptions :
  Caller     :
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_all_by_MethodLinkSpeciesSet ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Arg  2     : integer $limit_number [optional]
  Arg  3     : integer $limit_index_start [optional]
  Example    : my $genomic_align_trees =
                  $genomic_align_tree_adaptor->
                      fetch_all_by_MethodLinkSpeciesSet($mlss);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree objects. Objects 
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignTree objects.
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : none
  Status     : At risk
 
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public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_all_by_MethodLinkSpeciesSet_DnaFrag ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Arg  2     : Bio::EnsEMBL::Compara::DnaFrag $dnafrag
  Arg  3     : integer $start [optional, default = 1]
  Arg  4     : integer $end [optional, default = dnafrag_length]
  Arg  5     : integer $limit_number [optional, default = no limit]
  Arg  6     : integer $limit_index_start [optional, default = 0]
  Arg  7     : boolean $restrict_resulting_blocks [optional, default = no restriction]
  Example    : my $genomic_align_trees =
                  $genomic_align_tree_adaptor->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
                      $mlss, $dnafrag, 50000000, 50250000);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree objects. 
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignTree objects. Only dbID,
               adaptor and method_link_species_set are actually stored in the objects. The remaining
               attributes are only retrieved when requiered.
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : none
  Status     : At risk
 
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public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_all_by_MethodLinkSpeciesSet_Slice ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Arg  2     : Bio::EnsEMBL::Slice $original_slice
  Arg  3     : integer $limit_number [optional]
  Arg  4     : integer $limit_index_start [optional]
  Arg  5     : boolean $restrict_resulting_blocks [optional]
  Example    : my $genomic_align_trees =
                  $genomic_align_tree_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
                      $method_link_species_set, $original_slice);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree objects. The alignments may be
               reverse-complemented in order to match the strand of the original slice.
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignTree objects. Only dbID,
               adaptor and method_link_species_set are actually stored in the objects. The remaining
               attributes are only retrieved when required.
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : $object->method_name
  Status     : At risk
 
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public Reference Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_all_children_for_node ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : my $node = $self->adaptor->fetch_all_children_for_node($self);
  Description: Over-ride NestedSetAdaptor method for getting the all the children of a node
  Returntype : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions : throw if not Bio::EnsEMBL::Compara::NestedSet
  Caller     : 
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all_leaves_indexed ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all_roots ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_by_genomic_align_block_id ( )
  Arg  1     : integer $genomic_align_block_id
  Example    : my $genomic_align_tree =
                  $genomic_align_tree_adaptor->fetch_by_genomic_align_block_id($gab_id);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : $object->method_name
  Status     : At risk
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_by_GenomicAlignBlock ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignBlock $genomic_align_block
  Example    : my $genomic_align_tree =
                  $genomic_align_tree_adaptor->fetch_by_GenomicAlignBlock($genomic_align_block);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object. 
  Exceptions : Returns ref. to an empty array if no matching
               Bio::EnsEMBL::Compara::GenomicAlignTree object can be retrieved
  Caller     : $object->method_name
  Status     : At risk
 
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public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_first_shared_ancestor_indexed ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $node1
  Arg [2]    : Bio::EnsEMBL::Compara::NestedSet $node2
  Arg [n]    : Bio::EnsEMBL::Compara::NestedSet $node_n
  Example    : $lca = $nested_set_adaptor->fetch_first_shared_ancestor_indexed($node1, $node2);
  Description: Returns the first node of the tree that is an ancestor of all the nodes passed
               as arguments. There must be at least one argument, and all the nodes must share
               the same root
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : thrown if the nodes don't share the same root_id
 
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public Reference Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_node_by_node_id ( )
  Arg  1     : $node_id
  Example    : my $node = $self->adaptor->fetch_node_by_node_id($node_id);
  Description: Over-ride NestedSetAdaptor method for getting a node from its id
  Returntype : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions : throw if not Bio::EnsEMBL::Compara::NestedSet
  Caller     : 
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Reference Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_parent_for_node ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : my $parent = $self->adaptor->fetch_parent_for_node($self);
  Description: Over-ride NestedSetAdaptor method for getting the parent of a node
  Returntype : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions : throw if not Bio::EnsEMBL::Compara::NestedSet
  Caller     : 
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Reference Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::fetch_root_by_node ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : my $root = $self->adaptor->fetch_root_by_node($self);
  Description: Over-ride NestedSetAdaptor method for getting the root of a node
  Returntype : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions : throw if not Bio::EnsEMBL::Compara::NestedSet
  Caller     : 
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_subroot_by_left_right_index ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_subtree_under_node ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_tree_at_node_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::final_clause ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::init_instance_from_rowhash ( )
  Args[1]    : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Args[2]    : DBI::row_hashref $hashref containing key-value pairs
  Example    : $self->init_instance_from_rowhash($node, $rowhash);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::GenomicAlignTree object
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::left_join_clause ( )
  Args       : none
  Example    : none
  Description: a left join clause for use with generic_fetch
  Returntype : none
  Exceptions : none
  Caller     : NestedSetAdaptor::generic_fetch
  Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::new ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::set_neighbour_nodes_for_leaf ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Arg  2     : int $flanking
  Example    : $self->update_neighbourhood_data($node);
  Description: Update the left and right node_ids of a genomic_align_tree
               table in a database
  Returntype : none
  Exceptions : none
  Caller     : none
  Status     : At risk
 
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public Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::store ( )
  Arg 1       : Bio::EnsEMBL::Compara::GenomicAlignTree $root
  Arg[2]      : [optional] bool $skip_left_right_indexes
  Example     : $gata->store($root);
  Description : This method stores the GenomicAlign in the tree,
                the corresponding GenomicAlignBlock(s) and all
                the GenomicAlignTree nodes in this tree. If you set
                the $skip_left_right_indexes flag to any true value,
                the left and right indexes in the tree won't be build
                at this point. This may be useful for production
                purposes as building the indexes requires to lock the
                table and can hamper other processes storing data at
                that time.
                This method expects a structure like this:
                GENOMIC_ALIGN_TREE->

  • GENOMIC_ALIGN_GROUP->
    • GENOMIC_ALIGNs...
  • GENOMIC_ALIGN_TREE->
    • GENOMIC_ALIGN_GROUP->
      • GENOMIC_ALIGNs...
    • GENOMIC_ALIGN_TREE->
      • GENOMIC_ALIGN_GROUP->
        • GENOMIC_ALIGNs...
    • GENOMIC_ALIGN_TREE->
      • GENOMIC_ALIGN_GROUP->
        • GENOMIC_ALIGN...
  • GENOMIC_ALIGN_TREE->
    • GENOMIC_ALIGN_GROUP->
      • GENOMIC_ALIGN...
                I.e. each node has 1 GenomicAlignGroup containing 1 or
                more GenomicAligns and optionally 2 GenomicAlignTree objects
                representing the sub_nodes. These will also contain 1
                GenomicAlignGroup containing 1 or more GenomicAligns, etc.
                No GenomicAlignBlock is expected. These will be created
                and stored by this method.
  Exceptions  : throws if any of the nodes of the tree misses its
                GenomicAlign object or this one misses its
                GenomicAlignBlock objects.
  Caller      : general
  Status      : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::store_group ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : $genomic_align_tree_adaptor->store_group($genomic_align_tree);
  Description: Method for storing the group_id for a genomic_align_block. The
               group_id is set as the genomic_align_block_id of the first
               genomic_align object
  Returntype : none
  Exceptions : - cannot lock tables

 
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public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::store_node ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Example    : $genomic_align_tree_adaptor->store_node($genomic_align_tree);
  Description: Method for storing a single node. Called recursively.
  Returntype : none
  Exceptions : throw if no genomic_align_group ID has been set
  Caller     : none
  Status     : At risk
 
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public Nothing Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::sync_tree_leftright_index ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $root
  Arg [2]    : Boolean; indicates if you wish to use a fresh database 
               connection to perform any locking. If you are within an existing
               transaction this is a good idea to avoid locking the LR table
               for the duration of your transaction
  Example    : $nsa->sync_tree_leftright_index($root);
  Description: For the given root this method looks for left right index
               offset recorded in lr_index_offset for the configured
               table. The program locks on this table to reserve a batch
               of identifiers which are then used to left_right index
               the tree.
               The left right indexing is called by this method on your given
               tree root
  Returntype : Nothing
  Exceptions : Only raised from DBI problems
  Caller     : Public
 
Code:
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public List Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::tables ( )
  Args       : none
  Example    : $tables = $self->_tables()
  Description: a list of [tablename, alias] pairs for use with generic_fetch
  Returntype : list of [tablename, alias] pairs
  Exceptions : none
  Caller     : NestedSetAdaptor::generic_fetch
  Status     : At risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::update ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor::update_neighbourhood_data ( )
  Arg  1     : reference to Bio::EnsEMBL::Compara::GenomicAlignTree
  Arg  2     : boolean $no_recursivity
  Example    : $self->update_neighbourhood_data($node);
  Description: Update the left and right node_ids of a genomic_align_tree
               table in a database
  Returntype : none
  Exceptions : none
  Caller     : none
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::update_subtree ( ) [inherited]

Undocumented method

Code:
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The documentation for this class was generated from the following file: